Implement AlchemicalMolecule class

[richardjgowers]

Holds 2x Molecule and 1x AtomMapping

[IAlibay]

I assume here we need it to be both the topology & coordinates?

How about AlchemicalSystem? (unless we don't want to have the full system environment here? although long term we will need to support proteins to allow for side chain mutations)

How about:

• AtomMapping -> easily to obtain core, appearing, and disappearing atoms
• Two interchange objects for each state?
  • Since the API isn't very mature, short term: either two OpenMM System objects or two Parmed Structure objects? (maybe we should just jump the gun early here and go directly with the interchange API rather than waste time implementing a temporary solution?)

[dwhswenson]

What does this add beyond AtomMapping, since AtomMapping now includes the 2x Molecule? Does this still need to be an additional object?

[richardjgowers]

I think this isn't required since the Mapping got beefed up a little. I think AtomMapping is enough for edge descriptions.

[dwhswenson]

Moving to done as a "not going to do" -- we no longer see this as necessary.